Abubaker Patan

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Title(s)	Postdoctoral Scholar, School of Pharmacy and Pharmaceutical Science
School	Vc-health Sciences-schools
Address	9500 Gilman Drive # La Jolla CA 92093
vCard	Download vCard

Bibliographic

publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.

Bridging complexity and accessibility in metabolomics with MetaboApps. Nat Methods. 2026 Jul 24. Mannochio-Russo H, Gonçalves Nunes WD, Zhao HN, Kvitne KE, Xing S, Gouda H, Agongo J, Mohanty I, Charron-Lamoureux V, Rajkumar P, Pakkir Shah AK, Walter A, Krishnaraj R, El Abiead Y, Ferreira PC, Zuffa S, Patan A, Caraballo-Rodríguez AM, Bittremieux W, Petras D, Wang M, Dorrestein PC. PMID: 42498881.

View in: PubMed Mentions: Fields:
Cli Clinical Laboratory Techniques
Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles. Gut Microbes. 2026 Dec 31; 18(1):2690698. Zuffa S, Thomas SP, Patan A, Mohanty I, El Abiead Y, Deleray V, Kvitne KE, Kousha A, Suzuki E, Tsai CM, Nguyen G, Ho B, Y Liu G, Nizet V, Dorrestein PC, Askarian F, Tsunoda SM. PMID: 42374604; PMCID: PMC13321893.

View in: PubMed Mentions: Fields:
Gas Gastroenterology Mic Microbiology
Translation:Animals Cells
Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data. bioRxiv. 2026 Jun 26. Wang X, Patan A, Zhao HN, Charron-Lamoureux V, Shin Y, Petras D, Hong Y, Bowen BP, Northen TR, Dorrestein PC, Wang M. PMID: 42395381; PMCID: PMC13320852.

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A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models. Cell Rep. 2026 Jun 23; 45(6):117499. Zuffa S, Allaband C, Charron-Lamoureux V, Caraballo-Rodriguez AM, Patan A, Mohanty I, Agongo J, Bostick JW, Connerly TJ, Thron T, Needam BD, de Castro Fonseca M, Benitez RS, Hansen L, Tubb H, Cao J, Kalecký K, Bottiglieri T, MahmoudianDehkordi S, Schimmel L, Kueider-Paisley A, Graham SF, Siegel D, Wang M, Knight R, Kaddurah-Daouk R, Dorrestein PC, Mazmanian SK, Alzheimer Gut Microbiome Project Consortium. PMID: 42308105.

View in: PubMed Mentions: 1 Fields:
Cel Cell Biology Mol Molecular Biology
Translation:Humans Animals
Ordering molecular diversity in untargeted metabolomics via molecular community networking. Cell Rep Methods. 2026 Jul 20; 6(7):101468. Coler EA, Melnik A, Lotfi A, Moradi D, Ahiadu B, Portal Gomes PW, Patan A, Charron-Lamoureux V, Dorrestein PC, Barnes S, Boginski V, Semenov A, Aksenov AA. PMID: 42229419; PMCID: PMC13390073.

View in: PubMed Mentions: Fields:
Cel Cell Biology Mol Molecular Biology
Translation:Humans
Alkamines reveal a hidden layer of steroid and drug metabolism. bioRxiv. 2026 May 15. Agongo J, Panga SR, Xing S, Charron-Lamoureux V, Gouda H, Abiead YE, Nelson MR, Patan A, Terrazas MC, Kvitne KE, Seo JI, Rajkumar P, Giddings S, Mannochio-Russo H, Zemlin J, Mohanty I, Sala-Climent M, Hu Z, Delaray V, Yeboah SK, Zhao HN, Caraballo-Rodríguez AM, Williams CE, Williams CL, Gonçalves Nunes WD, Dorrestein K, Cao J, Shepherd I, Bock R, Roethler N, Jinich A, Burnett LA, Carver J, Devine RN, Arnatt CK, Murray IA, Knight R, Guma M, Hagey LR, Perdew G, Bandeira N, Wang M, Chu H, Siegel D, Dorrestein PC. PMID: 42182470; PMCID: PMC13192845.

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Structure-centric searching enables global mapping of the public metabolome. Nat Biotechnol. 2026 Apr 15. El Abiead Y, Seo JI, Charron-Lamoureux V, Strobel M, Gonçalves Nunes WD, Zhao HN, Kvitne KE, Zuffa S, Mannochio-Russo H, Gouda H, Bez C, Patan A, Xing S, Zemlin J, Mohany I, Agongo J, Caraballo Rodriguez AM, Burnett LA, Deleray V, Pakkir Shah AK, Kalinski JC, Petras D, Alygizakis N, Carver J, Yurekten O, Payne T, Fahy E, Subramaniam S, Vizcaíno JA, Wang M, Dorrestein PC. PMID: 41986697.

View in: PubMed Mentions: Fields:
Bio Biotechnology
Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome. bioRxiv. 2026 Apr 01. Kvitne KE, Zuffa S, Charron-Lamoureux V, Patan A, Agongo J, Cai J, Deleray V, El Abiead Y, Xing S, Zemlin J, Thomas S, Nelson MR, Gant A, Ghadishah A, Lam A, Ho B, Momper JD, Suhandynata RT, Bertrand K, Knight R, Chambers C, Dorrestein PC, Tsunoda SM. PMID: 41959458; PMCID: PMC13060235.

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Pan-Metabolomics Repository Mapping of the Carnitine Landscape. bioRxiv. 2026 Mar 31. Mannochio-Russo H, Ferreira PC, Kvitne KE, Patan A, Deleray V, Agongo J, Gouda H, Gonçalves Nunes WD, Xing S, Zemlin J, van Faassen M, Reilly ER, Koo I, Patterson AD, Tsunoda SM, Wang M, Siegel D, Burnett LA, Dorrestein PC. PMID: 41959195; PMCID: PMC13060134.

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Unlocking the Bile Acid Universe: Advanced Workflows and a Multidimensional Library of 280 Unique Species. bioRxiv. 2026 Feb 19. Zhang G, Vincent EC, Disselkoen SM, Dodds JN, DuVal-Smith Q, Patan A, Mohanty I, Deleray V, Zhang J, Thiessen PA, Bolton EE, Schymanski EL, Dorrestein PC, Theriot CM, Baker ES. PMID: 41756824; PMCID: PMC12934720.

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Navigating the conjugated metabolome. bioRxiv. 2026 Feb 09. Xing S, Patan A, Agongo J, Gouda H, Charron-Lamoureux V, El Abiead Y, Hu Z, Zhao HN, Mohanty I, Zemlin J, Nunes WDG, Burnett LA, Wang M, Siegel D, Dorrestein PC. PMID: 41727094; PMCID: PMC12919067.

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MS/MS Mass Spectrometry Filtering Tree for Bile Acid Regio- and Stereoisomer Annotation. Anal Chem. 2026 Feb 17; 98(6):4571-4584. Mohanty I, Xing S, Castillo V, Agongo J, Patan A, El Abiead Y, Mannochio-Russo H, Gonçalves Nunes WD, Zemlin J, Mizrahi I, Siegel D, Wang M, Hagey LR, Dorrestein PC. PMID: 41642850; PMCID: PMC12921657.

View in: PubMed Mentions: 1 Fields:
Che Chemistry Techniques
Translation:Animals
A searchable metadata network graph for microbiome metabolomics. bioRxiv. 2026 Feb 05. Charron-Lamoureux V, Xing S, Patan A, Walker C, Monter RA, Abiead YE, Zhao HN, Patel L, Weng Y, Gonzalez A, Ackermann G, Deleray V, Gandhi V, Mohanty I, Caraballo-Rodriguez AM, Kvitne KE, Zuffa S, Norman A, Martin A, Chin L, Paz-Gonzalez R, Sala-Climent M, Suryawinata N, Zemlin J, Gouda H, Hu Z, Norton G, Rajkumar P, Molina AJ, Bergstrom J, Pinner M, Giddings S, Aron AT, Liang L, Dahesh S, Lamichhane S, Reilly ER, Nizet V, Skrip A, Lukowski AL, Shore SFH, Ghoshal S, Engevik MA, Horvath TD, Renwick S, Agongo J, Marco ML, Mazmanian SK, Wang M, Yang H, McDonald D, Guma M, Stegmann E, Hernandez Perez N, Stincone P, Kemen E, Pakkir Shah AK, Bode L, Petras D, Siegel D, Raffatellu M, Patterson AD, Devkota S, Jinich A, Knight R, Zengler K, Dorrestein PC. PMID: 41676651; PMCID: PMC12889665.

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Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data. bioRxiv. 2026 Jan 26. Mannochio-Russo H, Gonçalves Nunes WD, Xing S, de Oliveira F, Caraballo-Rodríguez AM, Gomes PWP, Charron-Lamoureux V, Agongo J, Avalon NE, Bui T, Cancelada L, Chevrette MG, Cumsille A, de Araújo MB, De Graeve M, Deleray V, Donia MS, Dzveta MB, El Abiead Y, Ellis RJ, Franklin D, Garg N, Gouda H, Djande CYH, Hiskia A, Ho BN, Hughes CC, Hwang S, Iliakopoulou S, Iudicello JE, Jarmusch AK, Kaloudis T, Koester I, Konkel R, Koolen HHF, Kvitne KE, La Rosa SL, Lam A, Lamichhane S, Lephatsi M, Letendre S, Magyari S, Mazur-Marzec H, McDonald D, Mohanty I, Monge-Loría M, Moore DJ, Veiga TAM, Mulaudzi MS, Nephali L, Nguyen G, Orságh M, Patan A, Pluskal T, Pope PB, de Medeiros LS, Stincone P, Tekel A, Thomas S, Torres RR, Tsunoda SM, Tugizimana F, van Faassen M, Vasquez-Castro F, Vitale GA, Wagner BC, Wang CX, Zervou SK, Zhao HN, Zuffa S, Petras D, McCall LI, Knight R, Wang M, Dorrestein PC. PMID: 41659575; PMCID: PMC12874021.

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ChemEmbed: a deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings. Brief Bioinform. 2026 Jan 07; 27(1). Faizan-Khan M, Giné R, Badia JM, Pérez-Ribera M, Ruiz-Botella M, Junza A, Capellades J, Pérez-López I, Xing S, Patan A, Brugnara L, Novials A, Servitja JM, Vinaixa M, Dorrestein PC, Sales-Pardo M, Guimerà R, Yanes O. PMID: 41686648; PMCID: PMC12903953.

View in: PubMed Mentions: 2 Fields:
Com Computational Biology
Translation:Humans
Fecal microbial and metabolic signatures in children with very early onset inflammatory bowel disease. NPJ Biofilms Microbiomes. 2025 Dec 31; 12(1):33. Kvitne KE, Zuffa S, Charron-Lamoureux V, Mohanty I, Patan A, Mannochio-Russo H, Zemlin J, Burnett LA, Zhang LS, Cecala MC, Ersoz C, Connelly JA, Halasa N, Nicholson M, Dorrestein PC, Tsunoda SM, Markle J. PMID: 41476253; PMCID: PMC12864830.

View in: PubMed Mentions: Fields:
Mic Microbiology
Translation:Humans Cells
Microbiome-derived bile acid signatures in early life and their association with islet autoimmunity. Nat Commun. 2025 12 03; 17(1):38. Lamichhane S, Dickens AM, Buchacher T, Lou T, Charron-Lamoureux V, Kattelus R, Karmacharya P, da Silva LP, Kråkström M, Rasool O, Sen P, Walker C, Patan A, Gentry EC, Zuffa S, Arzoomand A, Lakshmikanth T, Mikeš J, Mebrahtu A, Vatanen T, Raffatellu M, Zengler K, Hyötyläinen T, Xavier RJ, Brodin P, Lahesmaa R, Dorrestein PC, Knip M, Orešic M. PMID: 41339624; PMCID: PMC12764907.

View in: PubMed Mentions: Fields:
Bio Biology Sci Science
Translation:Humans Cells
Environmental and maternal imprints on infant gut metabolic development. Cell Host Microbe. 2025 Dec 10; 33(12):2130-2147.e7. Kvitne KE, Allaband C, Onuora JC, Perry D, Zuffa S, Patel L, Charron-Lamoureux V, Mohanty I, Sejane K, Patan A, Mahmud AA, Ahmed T, Bassani DG, González A, Hamer DH, Haque R, Ho B, Hossain MI, Islam MS, McDonald D, Pell LG, Qamar H, Roth DE, Saha S, Shah PS, Siddiqui MM, Sarker SA, Sultana S, Thomas S, Burnett LA, Tsunoda SM, Bode L, Dorrestein PC, Knight R. PMID: 41308639; PMCID: PMC12875530.

View in: PubMed Mentions: Fields:
Mic Microbiology
Translation:Humans
Charting the Undiscovered Metabolome with Synthetic Multiplexing. bioRxiv. 2025 Nov 19. Patan A, Xing S, Charron-Lamoureux V, Hu Z, Deleray V, Agongo J, El Abiead Y, Mannochio-Russo H, Mohanty I, Gouda H, Zemlin J, Rajkumar P, Lee C, Leanos D, Weimann N, Tsuda W, Giddings S, Bui T, Kvitne KE, Zhao HN, Zuffa S, Nguyen V, Andrade A, Gonçalves Nunes WD, Caraballo-Rodríguez AM, Caetano David L, Carver J, Bandeira N, Wang M, Burnett LA, Siegel D, Dorrestein PC. PMID: 41332743; PMCID: PMC12667992.

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Environmental and Maternal Imprints on Infant Gut Metabolic Programming. bioRxiv. 2025 Jul 24. Kvitne KE, Allaband C, Onuora JC, Perry D, Zuffa S, Patel L, Charron-Lamoureux V, Mohanty I, Sejane K, Patan A, Al Mahmud A, Ahmed T, Bassani DG, González A, Hamer DH, Haque R, Ho B, Hossain MI, Islam MS, McDonald D, Pell LG, Qamar H, Roth DE, Saha S, Shah PS, Siddiqui MM, Sarker SA, Sultana S, Thomas S, Burnett LA, Tsunoda SM, Bode L, Dorrestein PC, Knight R. PMID: 40777448; PMCID: PMC12330730.

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The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids. Cell. 2025 Jul 24; 188(15):4154-4169.e19. Mannochio-Russo H, Charron-Lamoureux V, van Faassen M, Lamichhane S, Gonçalves Nunes WD, Deleray V, Ayala AV, Tanaka Y, Patan A, Vittali K, Rajkumar P, El Abiead Y, Zhao HN, Gomes PWP, Mohanty I, Lee C, Sund A, Sharma M, Liu Y, Pattynama D, Walker GT, Norton GJ, Khatib L, Andalibi MS, Wang CX, Ellis RJ, Moore DJ, Iudicello JE, Franklin D, Letendre S, Chin L, Walker C, Renwick S, Zemlin J, Meehan MJ, Song X, Kasper D, Burcham Z, Kim JJ, Kadakia S, Raffatellu M, Bode L, Chu H, Zengler K, Wang M, Siegel D, Knight R, Dorrestein PC. PMID: 40499541; PMCID: PMC12428309.

View in: PubMed Mentions: 10 Fields:
Cel Cell Biology
Translation:Humans
MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer Annotation. bioRxiv. 2025 Mar 09. Mohanty I, Xing S, Castillo V, Agongo J, Patan A, Abiead YE, Mannochio-Russo H, Zuffa S, Zemlin J, Tronel A, Gouellec AL, Soranzo T, Wang CX, Iudicello JE, Andalibi MS, Ellis RJ, Moore DJ, Franklin DR, Sala-Climent M, Guma M, Voigt RM, Kaddaruh-Dauok R, Siegel D, Wang M, Hagey LR, Dorrestein PC. PMID: 41659560; PMCID: PMC12874289.

View in: PubMed Mentions: 2
A guide to reverse metabolomics-a framework for big data discovery strategy. Nat Protoc. 2025 10; 20(10):2960-2993. Charron-Lamoureux V, Mannochio-Russo H, Lamichhane S, Xing S, Patan A, Portal Gomes PW, Rajkumar P, Deleray V, Caraballo-Rodríguez AM, Chua KV, Lee LS, Liu Z, Ching J, Wang M, Dorrestein PC. PMID: 40021805; PMCID: PMC12353464.

View in: PubMed Mentions: 5 Fields:
Cli Clinical Laboratory Techniques Sci Science
Translation:Humans Animals
Trajectories of microbiome-derived bile acids in early life - insights into the progression to islet autoimmunity. medRxiv. 2025 Feb 24. Lamichhane S, Dickens AM, Buchacher T, Lou ET, Charron-Lamoureux V, Kattelus R, Karmacharya P, Pinto da Silva L, Kråkström M, Rasool O, Sen P, Walker C, Patan A, Gentry EC, Arzoomand A, Lakshmikanth T, Mikeš J, Mebrahtu A, Vatanen T, Raffatellu M, Zengler K, Hyötyläinen T, Xavier RJ, Brodin P, Lahesmaa R, Dorrestein PC, Knip M, Orešic M. PMID: 40061321; PMCID: PMC11888530.

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The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds. bioRxiv. 2024 Nov 02. Mannochio-Russo H, Charron-Lamoureux V, van Faassen M, Lamichhane S, Nunes WDG, Deleray V, Patan A, Vittali K, Rajkumar P, El Abiead Y, Zhao HN, Gomes PWP, Mohanty I, Lee C, Sund A, Sharma M, Liu Y, Pattynama D, Walker GT, Norton GJ, Khatib L, Andalibi MS, Wang CX, Ellis RJ, Moore DJ, Iudicello JE, Franklin D, Letendre S, Chin L, Walker C, Renwick S, Zemlin J, Meehan MJ, Song X, Kasper D, Burcham Z, Kim JJ, Kadakia S, Raffatellu M, Bode L, Zengler K, Wang M, Siegel D, Knight R, Dorrestein PC. PMID: 39554097; PMCID: PMC11565975.

View in: PubMed Mentions:
Ordering molecular diversity in untargeted metabolomics via molecular community networking. bioRxiv. 2024 Aug 07. Coler EA, Melnik A, Lotfi A, Moradi D, Ahiadu B, Gomes PWP, Patan A, Dorrestein PC, Barnes S, Boginski V, Semenov A, Aksenov AA. PMID: 39131284; PMCID: PMC11312580.

View in: PubMed Mentions: